def run(argv):
opts = util.parse_docopt(__doc__, argv, False)
image = opts['<image>']
fastq_file = opts['--input']
contig_file = opts['--output']
task = opts['--task']
if not ctn.image_available(image):
util.err_exit('unknown_image', {'image': image})
cntr_src_dir = "/fastq"
biobox_yaml = fle.generate([
fle.fastq_arguments(cntr_src_dir, [fastq_file, "paired"])])
host_src_dir = os.path.abspath(os.path.dirname(fastq_file))
host_dst_dir = tmp.mkdtemp()
mount_strings = [
ctn.mount_string(host_src_dir, cntr_src_dir),
ctn.biobox_file_mount_string(fle.create_biobox_directory(biobox_yaml)),
ctn.output_directory_mount_string(host_dst_dir)]
ctn.run(ctn.create(image, task, mount_strings))
biobox_output = fle.parse(host_dst_dir)
copy_contigs_file(host_dst_dir, biobox_output, contig_file)
def run(argv):
opts = util.parse_docopt(__doc__, argv, False)
image = opts['<image>']
fastq_file = opts['--input']
contig_file = opts['--output']
task = opts['--task']
if not ctn.image_available(image):
util.err_exit('unknown_image', {'image': image})
cntr_src_dir = "/fastq"
biobox_yaml = fle.generate(
[fle.fastq_arguments(cntr_src_dir, [fastq_file, "paired"])])
host_src_dir = os.path.abspath(os.path.dirname(fastq_file))
host_dst_dir = tmp.mkdtemp()
mount_strings = [
ctn.mount_string(host_src_dir, cntr_src_dir),
ctn.biobox_file_mount_string(fle.create_biobox_directory(biobox_yaml)),
ctn.output_directory_mount_string(host_dst_dir)
]
ctn.run(ctn.create(image, task, mount_strings))
biobox_output = fle.parse(host_dst_dir)
copy_contigs_file(host_dst_dir, biobox_output, contig_file)
def test_checking_an_available_image_with_tag():
nose.assert_equal(ctn.image_available("python:2.7"), True)
def test_checking_an_available_image():
nose.assert_equal(ctn.image_available("python"), True)
def test_checking_an_available_image_with_tag():
nose.assert_equal(ctn.image_available("python:2.7"), True)
def test_checking_an_available_image():
nose.assert_equal(ctn.image_available("python"), True)